| Alkali Creek | Malheur, OR | 0 miles | SW |
| North Alkali Creek | Malheur, OR | 1.4 miles | SW |
| Allen Drain | Canyon, ID | 1.9 miles | NE |
| Johanson Drain | Canyon, ID | 3.1 miles | NE |
| Imbler Drain | Canyon, ID | 4.1 miles | NE |
| Imbler Drain | Canyon, OR | 4.1 miles | NE |
| Parkins Drain | Owyhee, ID | 5.1 miles | SE |
| Succor Creek | Malheur, ID | 6.4 miles | SE |
| Succor Creek | Malheur, OR | 6.4 miles | SE |
| Succor Creek | Owyhee, ID | 6.4 miles | SE |
| Succor Creek | Owyhee, OR | 6.4 miles | SE |
| Sage Creek | Owyhee, ID | 6.6 miles | SE |
| Sage Creek | Owyhee, OR | 6.6 miles | SE |
| South Alkali Creek | Malheur, OR | 7.5 miles | SW |
| Sand Hollow Creek | Malheur, OR | 7.6 miles | NW |
| Camp Kettle Creek | Malheur, OR | 8.9 miles | SW |
| Keck Slough | Malheur, OR | 9.2 miles | NE |
| Dixie Slough | Canyon, ID | 9.3 miles | NE |
| Parma Drain | Canyon, ID | 9.4 miles | NE |
| North Branch Camp Kettle Creek | Malheur, OR | 9.6 miles | SW |
| South Branch Camp Kettle Creek | Malheur, OR | 9.6 miles | SW |
| Owyhee River | Malheur, ID | 9.6 miles | NE |
| Owyhee River | Malheur, NV | 9.6 miles | NE |
| Owyhee River | Malheur, OR | 9.6 miles | NE |
| Jump Creek | Owyhee, ID | 9.8 miles | SE |
| Gordon Creek | Malheur, OR | 9.8 miles | SW |
| Lone Willow Creek | Malheur, OR | 9.9 miles | NW |
| Rock Spring Creek | Malheur, OR | 9.9 miles | NW |
| Boise River | Canyon, ID | 10.1 miles | NE |
| Sand Hollow Creek | Canyon, ID | 10.7 miles | NE |
| Birch Creek | Malheur, OR | 10.9 miles | SW |
| Indian Creek | Malheur, OR | 10.9 miles | SW |
| Sage Creek | Malheur, OR | 12.5 miles | SW |
| Poison Creek | Owyhee, ID | 12.5 miles | SE |
| Jenson Drain | Owyhee, ID | 12.8 miles | SE |
| Deer Creek | Malheur, OR | 13.1 miles | SW |
| Little Poison Creek | Owyhee, ID | 14.4 miles | SE |
| Little Poison Creek | Owyhee, OR | 14.4 miles | SE |
| Sheep Creek | Malheur, OR | 14.7 miles | NE |
| South Sheep Creek | Malheur, OR | 14.7 miles | NE |
| Wild Horse Creek | Malheur, OR | 15.3 miles | SW |
| Trimbly Creek | Malheur, OR | 15.6 miles | SW |
| Cherry Creek | Malheur, OR | 16 miles | SW |
| Dry Creek | Malheur, OR | 16.8 miles | SW |
| Falice Creek | Malheur, OR | 16.9 miles | SW |
| Rookie Creek | Malheur, OR | 17 miles | SW |
| Indian Creek | Ada, ID | 17.6 miles | NE |
| Bridge Creek | Owyhee, ID | 17.7 miles | SE |
| Hoodoo Creek | Malheur, OR | 18.1 miles | NW |
| Twin Springs Creek | Malheur, OR | 18.9 miles | SW |
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